Photograph courtesy Beth Shapiro
Beth Shapiro travels through time—observing mammoths, dodos, and other extinct animals; witnessing the last ice age and arrival of humans in North America; watching genetic diversity shrink in one species while blossoming in another.
Her journey is made possible by ancient DNA samples and statistical models that give science a whole new view of our tumultuous past.
This very new field uses genetic information gleaned from ancient animals and plants to discover how evolution happens over time and territory. By analyzing DNA samples from species at not just one, but many moments in time, researchers can trace changes in populations, and overlay those changes with concurrent environmental events. The precision this allows is unprecedented.
“We can pinpoint when a species’ genetic diversity changed.” Shapiro says. “We can see if that change may have been influenced by a specific event such as a new predator or shift in climate. By sampling populations across time, we can actually see diversity being lost or gained as animals evolve and migrate.”
“There have been many hypotheses about why populations maintain or lose diversity.” she explains, “Now, for the first time, ancient DNA lets us explicitly test those hypotheses and propose new ones. Answering these questions can help form strategies to protect and conserve species today. We can look at prehistoric analogs to modern populations and see who was in trouble, when, and why. We can measure which environmental or habitat factors were most important in determining the fate of different species, and how those factors influenced each other. For example, if we identify a time when horses were doing particularly well, we can extract ancient plant DNA from the soil and scrutinize vegetation they grazed on.”
Already, ancient DNA has proved several long-standing assumptions wrong. “It was commonly accepted that the reason bison have no diversity today is that almost all of them were killed by human hunters in North America 200 years ago,” Shapiro notes.
Instead, her ancient DNA analysis proved that even when there were millions of bison, they had no genetic diversity. In fact, their decline began not 200, but 35,000 years ago as climate changed and they passed through the peak of the last ice age.
Ancient DNA also sheds new light on the decades-old debate over what caused the mass extinctions of mammoths, saber-toothed cats, mastodons, and other distinctive species about 10,000 years ago. Some scientists argue that the arrival of humans and overhunting triggered the extinctions; others attribute the event to major changes in vegetation and climate.
Surprising new ancient DNA findings reveal that the true beginning of this massive extinction was well before human intervention or the peak of the last ice age. As Shapiro notes, “Suddenly we realize that all the species we have data on began declining 35,000 to 50,000 years ago. Understanding that period has never been a scientific priority. But now we see that something very important was happening at that time which ultimately determined the outcome of many different animals.”
If analyzing ancient DNA is an adventure, so is gathering it. Shapiro has scoured remote landscapes in Alaska, Kenya, Siberia, and Canada to collect small samples from bones, teeth, skulls, and tusks that will be brought back to the lab, ground up, dissolved, altered and "cooked" so DNA can be extracted.
Shapiro’s ongoing expeditions to gold fields in Canada’s Yukon Territory have proved especially fruitful. Good relationships with numerous mining companies there permit her team to gather bone samples exposed as miner’s high-pressure hoses wash permafrost away. What makes these samples especially valuable is the ability to date them to earlier periods than traditional radiocarbon methods allow.
“Radiocarbon dates,” she explains, “can only go back about 40,000 to 50,000 years. But these Yukon sites give us a unique chance to establish the age of samples as far back as 130,000 years.”
How? For millennia, layers of volcanic ash have settled in sites being mined today. These layers can be linked to specific eruptions that occurred prior to the time registered by radiocarbon dating. “Let’s say we know an eruption happened about 80,000 years ago. If we find bones associated with that volcanic ash layer, we know they’re that old too," she says. "This lets us push back population genetics estimates to older and older time periods than ever before.”
What does the future hold for a scientist who spends her days peering into the past? “We’re now able to look not only at particular genes, but at how whole genomes—the entirety of a species’ genetics—evolved. We can go beyond mitochondrial DNA to nuclear DNA, which gives us an entirely new set of evolutionary information. We can see how genetic traits changed through time and how natural selection happened in real populations. I think we’re on the brink of the most exciting time ever in this field.”
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